[2024-01-24 11:26:36,719] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:36,721] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:36,721] [INFO] DQC Reference Directory: /var/lib/cwl/stgee7a551a-c755-4efb-b4b2-b27ba7561890/dqc_reference
[2024-01-24 11:26:37,947] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:37,947] [INFO] Task started: Prodigal
[2024-01-24 11:26:37,948] [INFO] Running command: gunzip -c /var/lib/cwl/stg783d6868-13b9-415d-9fb3-7db643798d44/GCF_014648915.1_ASM1464891v1_genomic.fna.gz | prodigal -d GCF_014648915.1_ASM1464891v1_genomic.fna/cds.fna -a GCF_014648915.1_ASM1464891v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:06,263] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:06,263] [INFO] Task started: HMMsearch
[2024-01-24 11:27:06,263] [INFO] Running command: hmmsearch --tblout GCF_014648915.1_ASM1464891v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee7a551a-c755-4efb-b4b2-b27ba7561890/dqc_reference/reference_markers.hmm GCF_014648915.1_ASM1464891v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:06,666] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:06,668] [INFO] Found 6/6 markers.
[2024-01-24 11:27:06,746] [INFO] Query marker FASTA was written to GCF_014648915.1_ASM1464891v1_genomic.fna/markers.fasta
[2024-01-24 11:27:06,746] [INFO] Task started: Blastn
[2024-01-24 11:27:06,746] [INFO] Running command: blastn -query GCF_014648915.1_ASM1464891v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee7a551a-c755-4efb-b4b2-b27ba7561890/dqc_reference/reference_markers.fasta -out GCF_014648915.1_ASM1464891v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:08,045] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:08,049] [INFO] Selected 21 target genomes.
[2024-01-24 11:27:08,049] [INFO] Target genome list was writen to GCF_014648915.1_ASM1464891v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:08,056] [INFO] Task started: fastANI
[2024-01-24 11:27:08,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg783d6868-13b9-415d-9fb3-7db643798d44/GCF_014648915.1_ASM1464891v1_genomic.fna.gz --refList GCF_014648915.1_ASM1464891v1_genomic.fna/target_genomes.txt --output GCF_014648915.1_ASM1464891v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:57,848] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:57,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee7a551a-c755-4efb-b4b2-b27ba7561890/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:57,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee7a551a-c755-4efb-b4b2-b27ba7561890/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:57,864] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:57,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:57,864] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	100.0	3421	3427	95	conclusive
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	87.8862	2271	3427	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	87.8386	1844	3427	95	below_threshold
Streptomyces asoensis	strain=JCM 4185	GCA_014649075.1	249586	249586	type	True	87.0425	2177	3427	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	86.9823	2181	3427	95	below_threshold
Streptomyces galilaeus	strain=ATCC 14969	GCA_008704575.1	33899	33899	type	True	86.8369	2043	3427	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	86.7883	2088	3427	95	below_threshold
Streptomyces humidus	strain=JCM 4386	GCA_014649655.1	52259	52259	type	True	86.4829	1993	3427	95	below_threshold
Streptomyces adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	85.4752	1905	3427	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.4155	2117	3427	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	85.127	1984	3427	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.0491	1925	3427	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.9145	1830	3427	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.8707	1760	3427	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	84.6535	2061	3427	95	below_threshold
Streptomyces griseochromogenes	strain=DSM 40499	GCA_017874495.1	68214	68214	type	True	84.5054	1990	3427	95	below_threshold
Streptomyces griseochromogenes	strain=ATCC 14511	GCA_001542625.2	68214	68214	type	True	84.4812	1978	3427	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	84.3062	1892	3427	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	83.9243	1872	3427	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	83.8663	1878	3427	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	83.6046	1926	3427	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:57,866] [INFO] DFAST Taxonomy check result was written to GCF_014648915.1_ASM1464891v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:57,866] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:57,866] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:57,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee7a551a-c755-4efb-b4b2-b27ba7561890/dqc_reference/checkm_data
[2024-01-24 11:27:57,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:57,965] [INFO] Task started: CheckM
[2024-01-24 11:27:57,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648915.1_ASM1464891v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648915.1_ASM1464891v1_genomic.fna/checkm_input GCF_014648915.1_ASM1464891v1_genomic.fna/checkm_result
[2024-01-24 11:30:22,471] [INFO] Task succeeded: CheckM
[2024-01-24 11:30:22,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:30:22,501] [INFO] ===== Completeness check finished =====
[2024-01-24 11:30:22,501] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:30:22,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648915.1_ASM1464891v1_genomic.fna/markers.fasta)
[2024-01-24 11:30:22,502] [INFO] Task started: Blastn
[2024-01-24 11:30:22,502] [INFO] Running command: blastn -query GCF_014648915.1_ASM1464891v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee7a551a-c755-4efb-b4b2-b27ba7561890/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648915.1_ASM1464891v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:30:24,548] [INFO] Task succeeded: Blastn
[2024-01-24 11:30:24,553] [INFO] Selected 18 target genomes.
[2024-01-24 11:30:24,553] [INFO] Target genome list was writen to GCF_014648915.1_ASM1464891v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:30:24,573] [INFO] Task started: fastANI
[2024-01-24 11:30:24,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg783d6868-13b9-415d-9fb3-7db643798d44/GCF_014648915.1_ASM1464891v1_genomic.fna.gz --refList GCF_014648915.1_ASM1464891v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648915.1_ASM1464891v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:31:10,067] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:10,094] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:31:10,094] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014648915.1	s__Streptomyces phaeofaciens	100.0	3421	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002019855.1	s__Streptomyces antibioticus_B	89.7581	2234	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.20	96.76	0.94	0.90	5	-
GCF_001514205.1	s__Streptomyces griseoruber	87.8922	2267	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013085465.1	s__Streptomyces cacaoi_A	87.8847	2298	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001298545.1	s__Streptomyces sp001298545	87.842	2336	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.23	95.13	0.87	0.84	4	-
GCF_001184025.1	s__Streptomyces sp001184025	87.6886	2139	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.49	98.49	0.84	0.84	2	-
GCF_900129855.1	s__Streptomyces sp900129855	87.5315	2101	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.68	99.68	0.97	0.97	2	-
GCF_004363835.1	s__Streptomyces sp004363835	87.4937	2239	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	87.2257	2222	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016860545.1	s__Streptomyces asoensis	87.0467	2170	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.07	98.15	0.93	0.87	3	-
GCF_001746365.1	s__Streptomyces sp001746365	86.8641	2043	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013044505.1	s__Streptomyces sp013044505	85.5691	1996	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377175.1	s__Streptomyces adustus	85.434	1912	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718165.1	s__Streptomyces fulvoviolaceus	85.3051	2102	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282115.1	s__Streptomyces sp001282115	85.2637	1767	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	0.95	0.95	2	-
GCF_002242805.1	s__Streptomyces diastatochromogenes	85.0925	2108	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.15	97.09	0.86	0.86	5	-
GCF_000376565.1	s__Streptomyces hokutonensis	84.6376	2063	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.37	96.37	0.82	0.82	2	-
GCF_001280015.1	s__Streptomyces sp001280015	84.4478	1881	3427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:31:10,096] [INFO] GTDB search result was written to GCF_014648915.1_ASM1464891v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:31:10,096] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:31:10,102] [INFO] DFAST_QC result json was written to GCF_014648915.1_ASM1464891v1_genomic.fna/dqc_result.json
[2024-01-24 11:31:10,102] [INFO] DFAST_QC completed!
[2024-01-24 11:31:10,103] [INFO] Total running time: 0h4m33s